Variant report

Variant	rs3817575
Chromosome Location	chr7:70249868-70249869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:70249833-70251108	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr7:70249771-70252077	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:70249816-70251081	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
AUTS2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10228883	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10264980	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10499822	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12698936	0.89[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17763090	0.96[ASN][1000 genomes]
rs2293501	0.81[JPT][hapmap]
rs2293503	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2293504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460557	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948548	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6959590	0.86[JPT][hapmap]
rs6959597	0.86[JPT][hapmap]
rs6971633	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7781211	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs951391	0.86[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9886083	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9886351	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3341834	chr7:69968031-70288098	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1025164	chr7:70061655-70469358	Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538931	chr7:70061655-70469358	Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1017876	chr7:70073764-70434599	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1022747	chr7:70169254-70301285	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv429771	chr7:70188375-70294296	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028853	chr7:70211620-70523331	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv533212	chr7:70220687-70511129	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1022759	chr7:70236919-70292317	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv888341	chr7:70249358-70316365	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70214800-70250000	Weak transcription	Psoas Muscle	Psoas
2	chr7:70222000-70258000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:70226400-70254800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:70227400-70253000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:70228400-70250000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:70228400-70257400	Weak transcription	Right Atrium	heart
7	chr7:70229400-70259600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr7:70229400-70259600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr7:70230200-70254000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:70230200-70257400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr7:70230600-70250000	Weak transcription	Right Ventricle	heart
12	chr7:70231000-70250000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:70231600-70250000	Weak transcription	NHLF	lung
14	chr7:70232000-70250000	Weak transcription	Pancreas	Pancrea
15	chr7:70232000-70250000	Weak transcription	HMEC	breast
16	chr7:70233400-70250200	Weak transcription	Colonic Mucosa	Colon
17	chr7:70234600-70259600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:70235200-70258200	Strong transcription	HSMMtube	muscle
19	chr7:70236400-70250000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:70236400-70257000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:70236800-70258200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:70238400-70250000	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:70238600-70259600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:70238800-70259600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:70239200-70259400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr7:70239800-70259400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:70240200-70257000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:70240200-70258000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:70240800-70259200	Strong transcription	Fetal Intestine Small	intestine
30	chr7:70241000-70259200	Strong transcription	Aorta	Aorta
31	chr7:70241200-70257200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:70241400-70256400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr7:70241400-70257400	Strong transcription	HSMM	muscle
34	chr7:70241800-70257200	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr7:70241800-70259400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:70242000-70252600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:70242000-70257200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:70242200-70250000	Weak transcription	Fetal Heart	heart
39	chr7:70242200-70259600	Strong transcription	Dnd41	blood
40	chr7:70242200-70259600	Weak transcription	NHDF-Ad	bronchial
41	chr7:70242600-70250400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr7:70243200-70259600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:70243600-70259600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:70243800-70258200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:70243800-70258200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:70244200-70256000	Strong transcription	Lung	lung
47	chr7:70244200-70256400	Strong transcription	Ovary	ovary
48	chr7:70244400-70251000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:70244800-70259200	Strong transcription	GM12878-XiMat	blood
50	chr7:70245200-70251600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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